niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/convex_hull.py

@@ -0,0 +1,386 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CONVEX_HULL_METADATA = Metadata(
+    id="945c8df244e1356a8e523e12b46e0aa912eddb4c.boutiques",
+    name="ConvexHull",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ConvexHullParameters = typing.TypedDict('ConvexHullParameters', {
+    "__STYX_TYPE__": typing.Literal["ConvexHull"],
+    "vol": typing.NotRequired[InputPathType | None],
+    "isoval": typing.NotRequired[float | None],
+    "isorange": typing.NotRequired[list[float] | None],
+    "isocmask": typing.NotRequired[str | None],
+    "xform": typing.NotRequired[str | None],
+    "surface_input": typing.NotRequired[InputPathType | None],
+    "surf_vol": typing.NotRequired[InputPathType | None],
+    "input_1d": typing.NotRequired[InputPathType | None],
+    "q_opt": typing.NotRequired[str | None],
+    "proj_xy": bool,
+    "orig_coord": bool,
+    "these_coords": typing.NotRequired[InputPathType | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[str | None],
+    "novolreg": bool,
+    "setenv": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ConvexHull": convex_hull_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "ConvexHull": convex_hull_outputs,
+    }.get(t)
+
+
+class ConvexHullOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `convex_hull(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_surf: OutputPathType | None
+    """Output surface file"""
+
+
+def convex_hull_params(
+    vol: InputPathType | None = None,
+    isoval: float | None = None,
+    isorange: list[float] | None = None,
+    isocmask: str | None = None,
+    xform: str | None = None,
+    surface_input: InputPathType | None = None,
+    surf_vol: InputPathType | None = None,
+    input_1d: InputPathType | None = None,
+    q_opt: str | None = None,
+    proj_xy: bool = False,
+    orig_coord: bool = False,
+    these_coords: InputPathType | None = None,
+    output_prefix: str | None = None,
+    debug: str | None = None,
+    novolreg: bool = False,
+    setenv: str | None = None,
+) -> ConvexHullParameters:
+    """
+    Build parameters.
+    
+    Args:
+        vol: Input AFNI (or AFNI readable) volume.
+        isoval: Create isosurface where volume = V.
+        isorange: Create isosurface where V0 <= volume < V1.
+        isocmask: Create isosurface where MASK_COM != 0. Example: -isocmask '-a\
+            VOL+orig -expr (1-bool(a-V))' is equivalent to using -isoval V. NOTE:\
+            Allowed only with -xform mask.
+        xform: Transform to apply to volume values before searching for sign\
+            change boundary. Options: mask, shift, none.
+        surface_input: Input surface type.
+        surf_vol: Specify a surface volume which contains a transform to apply\
+            to the surface node coordinates.
+        input_1d: Construct the triangulation of the points contained in 1D\
+            file XYZ. Use AFNI's [] selectors to specify the XYZ columns.
+        q_opt: Meshing option OPT. Options: convex_hull, triangulate_xy.
+        proj_xy: Project points onto plane whose normal is the third principal\
+            component. Then rotate projection so that plane is parallel to Z =\
+            constant.
+        orig_coord: Use original coordinates when writing surface, not\
+            transformed ones.
+        these_coords: Use coordinates in COORDS.1D when writing surface.
+        output_prefix: Prefix of output surface. Specifies the format and\
+            prefix of the surface.
+        debug: Debugging level.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        setenv: Set environment variable ENVname to be ENVvalue.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ConvexHull",
+        "proj_xy": proj_xy,
+        "orig_coord": orig_coord,
+        "novolreg": novolreg,
+    }
+    if vol is not None:
+        params["vol"] = vol
+    if isoval is not None:
+        params["isoval"] = isoval
+    if isorange is not None:
+        params["isorange"] = isorange
+    if isocmask is not None:
+        params["isocmask"] = isocmask
+    if xform is not None:
+        params["xform"] = xform
+    if surface_input is not None:
+        params["surface_input"] = surface_input
+    if surf_vol is not None:
+        params["surf_vol"] = surf_vol
+    if input_1d is not None:
+        params["input_1d"] = input_1d
+    if q_opt is not None:
+        params["q_opt"] = q_opt
+    if these_coords is not None:
+        params["these_coords"] = these_coords
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if debug is not None:
+        params["debug"] = debug
+    if setenv is not None:
+        params["setenv"] = setenv
+    return params
+
+
+def convex_hull_cargs(
+    params: ConvexHullParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("ConvexHull")
+    if params.get("vol") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("vol"))
+        ])
+    if params.get("isoval") is not None:
+        cargs.extend([
+            "-isoval",
+            str(params.get("isoval"))
+        ])
+    if params.get("isorange") is not None:
+        cargs.extend([
+            "-isorange",
+            *map(str, params.get("isorange"))
+        ])
+    if params.get("isocmask") is not None:
+        cargs.extend([
+            "-isocmask",
+            params.get("isocmask")
+        ])
+    if params.get("xform") is not None:
+        cargs.extend([
+            "-xform",
+            params.get("xform")
+        ])
+    if params.get("surface_input") is not None:
+        cargs.extend([
+            "-i_TYPE",
+            execution.input_file(params.get("surface_input"))
+        ])
+    if params.get("surf_vol") is not None:
+        cargs.extend([
+            "-sv",
+            execution.input_file(params.get("surf_vol"))
+        ])
+    if params.get("input_1d") is not None:
+        cargs.extend([
+            "-input_1D",
+            execution.input_file(params.get("input_1d"))
+        ])
+    if params.get("q_opt") is not None:
+        cargs.extend([
+            "-q_opt",
+            params.get("q_opt")
+        ])
+    if params.get("proj_xy"):
+        cargs.append("-proj_xy")
+    if params.get("orig_coord"):
+        cargs.append("-orig_coord")
+    if params.get("these_coords") is not None:
+        cargs.extend([
+            "-these_coords",
+            execution.input_file(params.get("these_coords"))
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-o_TYPE",
+            params.get("output_prefix")
+        ])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            params.get("debug")
+        ])
+    if params.get("novolreg"):
+        cargs.append("-novolreg")
+    if params.get("setenv") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("setenv")
+        ])
+    return cargs
+
+
+def convex_hull_outputs(
+    params: ConvexHullParameters,
+    execution: Execution,
+) -> ConvexHullOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = ConvexHullOutputs(
+        root=execution.output_file("."),
+        out_surf=execution.output_file(params.get("output_prefix")) if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def convex_hull_execute(
+    params: ConvexHullParameters,
+    execution: Execution,
+) -> ConvexHullOutputs:
+    """
+    A program to find the convex hull, or perform a Delaunay triangulation of a set
+    of points.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ConvexHullOutputs`).
+    """
+    params = execution.params(params)
+    cargs = convex_hull_cargs(params, execution)
+    ret = convex_hull_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def convex_hull(
+    vol: InputPathType | None = None,
+    isoval: float | None = None,
+    isorange: list[float] | None = None,
+    isocmask: str | None = None,
+    xform: str | None = None,
+    surface_input: InputPathType | None = None,
+    surf_vol: InputPathType | None = None,
+    input_1d: InputPathType | None = None,
+    q_opt: str | None = None,
+    proj_xy: bool = False,
+    orig_coord: bool = False,
+    these_coords: InputPathType | None = None,
+    output_prefix: str | None = None,
+    debug: str | None = None,
+    novolreg: bool = False,
+    setenv: str | None = None,
+    runner: Runner | None = None,
+) -> ConvexHullOutputs:
+    """
+    A program to find the convex hull, or perform a Delaunay triangulation of a set
+    of points.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        vol: Input AFNI (or AFNI readable) volume.
+        isoval: Create isosurface where volume = V.
+        isorange: Create isosurface where V0 <= volume < V1.
+        isocmask: Create isosurface where MASK_COM != 0. Example: -isocmask '-a\
+            VOL+orig -expr (1-bool(a-V))' is equivalent to using -isoval V. NOTE:\
+            Allowed only with -xform mask.
+        xform: Transform to apply to volume values before searching for sign\
+            change boundary. Options: mask, shift, none.
+        surface_input: Input surface type.
+        surf_vol: Specify a surface volume which contains a transform to apply\
+            to the surface node coordinates.
+        input_1d: Construct the triangulation of the points contained in 1D\
+            file XYZ. Use AFNI's [] selectors to specify the XYZ columns.
+        q_opt: Meshing option OPT. Options: convex_hull, triangulate_xy.
+        proj_xy: Project points onto plane whose normal is the third principal\
+            component. Then rotate projection so that plane is parallel to Z =\
+            constant.
+        orig_coord: Use original coordinates when writing surface, not\
+            transformed ones.
+        these_coords: Use coordinates in COORDS.1D when writing surface.
+        output_prefix: Prefix of output surface. Specifies the format and\
+            prefix of the surface.
+        debug: Debugging level.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        setenv: Set environment variable ENVname to be ENVvalue.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ConvexHullOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVEX_HULL_METADATA)
+    params = convex_hull_params(
+        vol=vol,
+        isoval=isoval,
+        isorange=isorange,
+        isocmask=isocmask,
+        xform=xform,
+        surface_input=surface_input,
+        surf_vol=surf_vol,
+        input_1d=input_1d,
+        q_opt=q_opt,
+        proj_xy=proj_xy,
+        orig_coord=orig_coord,
+        these_coords=these_coords,
+        output_prefix=output_prefix,
+        debug=debug,
+        novolreg=novolreg,
+        setenv=setenv,
+    )
+    return convex_hull_execute(params, execution)
+
+
+__all__ = [
+    "CONVEX_HULL_METADATA",
+    "ConvexHullOutputs",
+    "ConvexHullParameters",
+    "convex_hull",
+    "convex_hull_params",
+]

niwrap_afni/afni/count.py

@@ -0,0 +1,327 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+COUNT_METADATA = Metadata(
+    id="d518eb3cafe76c3d60b5e88beee05f05e59c9422.boutiques",
+    name="count",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+CountParameters = typing.TypedDict('CountParameters', {
+    "__STYX_TYPE__": typing.Literal["count"],
+    "bot": str,
+    "top": str,
+    "step": typing.NotRequired[str | None],
+    "seed": typing.NotRequired[float | None],
+    "sseed": typing.NotRequired[str | None],
+    "column": bool,
+    "digits": typing.NotRequired[float | None],
+    "form": typing.NotRequired[str | None],
+    "root": typing.NotRequired[str | None],
+    "sep": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "scale": typing.NotRequired[float | None],
+    "comma": bool,
+    "skipnmodm": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "count": count_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class CountOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `count(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def count_params(
+    bot: str,
+    top: str,
+    step: str | None = None,
+    seed: float | None = None,
+    sseed: str | None = None,
+    column: bool = False,
+    digits: float | None = None,
+    form: str | None = None,
+    root: str | None = None,
+    sep: str | None = None,
+    suffix: str | None = None,
+    scale: float | None = None,
+    comma: bool = False,
+    skipnmodm: str | None = None,
+) -> CountParameters:
+    """
+    Build parameters.
+    
+    Args:
+        bot: Starting number or character.
+        top: Ending number or character.
+        step: Stride step or mode (integer step size, R#, S# or S).
+        seed: Seed number for random number generator.
+        sseed: Seed string for random number generator.
+        column: Write output, one number per line.
+        digits: Number of digits to print.
+        form: Custom format string for printing the numbers.
+        root: String to print before the number.
+        sep: Separator character between the numbers.
+        suffix: String to print after the number.
+        scale: Scale factor to multiply each number.
+        comma: Put commas between the outputs.
+        skipnmodm: Skip numbers with modulus.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "count",
+        "bot": bot,
+        "top": top,
+        "column": column,
+        "comma": comma,
+    }
+    if step is not None:
+        params["step"] = step
+    if seed is not None:
+        params["seed"] = seed
+    if sseed is not None:
+        params["sseed"] = sseed
+    if digits is not None:
+        params["digits"] = digits
+    if form is not None:
+        params["form"] = form
+    if root is not None:
+        params["root"] = root
+    if sep is not None:
+        params["sep"] = sep
+    if suffix is not None:
+        params["suffix"] = suffix
+    if scale is not None:
+        params["scale"] = scale
+    if skipnmodm is not None:
+        params["skipnmodm"] = skipnmodm
+    return params
+
+
+def count_cargs(
+    params: CountParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("count")
+    cargs.append(params.get("bot"))
+    cargs.append(params.get("top"))
+    if params.get("step") is not None:
+        cargs.append(params.get("step"))
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("seed"))
+        ])
+    if params.get("sseed") is not None:
+        cargs.extend([
+            "-sseed",
+            params.get("sseed")
+        ])
+    if params.get("column"):
+        cargs.append("-column")
+    if params.get("digits") is not None:
+        cargs.extend([
+            "-digits",
+            str(params.get("digits"))
+        ])
+    if params.get("form") is not None:
+        cargs.extend([
+            "-form",
+            params.get("form")
+        ])
+    if params.get("root") is not None:
+        cargs.extend([
+            "-root",
+            params.get("root")
+        ])
+    if params.get("sep") is not None:
+        cargs.extend([
+            "-sep",
+            params.get("sep")
+        ])
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "-scale",
+            str(params.get("scale"))
+        ])
+    if params.get("comma"):
+        cargs.append("-comma")
+    if params.get("skipnmodm") is not None:
+        cargs.extend([
+            "-skipnmodm",
+            params.get("skipnmodm")
+        ])
+    return cargs
+
+
+def count_outputs(
+    params: CountParameters,
+    execution: Execution,
+) -> CountOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = CountOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def count_execute(
+    params: CountParameters,
+    execution: Execution,
+) -> CountOutputs:
+    """
+    Numbered copies generator with custom format support and random sequence
+    options.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `CountOutputs`).
+    """
+    params = execution.params(params)
+    cargs = count_cargs(params, execution)
+    ret = count_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def count(
+    bot: str,
+    top: str,
+    step: str | None = None,
+    seed: float | None = None,
+    sseed: str | None = None,
+    column: bool = False,
+    digits: float | None = None,
+    form: str | None = None,
+    root: str | None = None,
+    sep: str | None = None,
+    suffix: str | None = None,
+    scale: float | None = None,
+    comma: bool = False,
+    skipnmodm: str | None = None,
+    runner: Runner | None = None,
+) -> CountOutputs:
+    """
+    Numbered copies generator with custom format support and random sequence
+    options.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        bot: Starting number or character.
+        top: Ending number or character.
+        step: Stride step or mode (integer step size, R#, S# or S).
+        seed: Seed number for random number generator.
+        sseed: Seed string for random number generator.
+        column: Write output, one number per line.
+        digits: Number of digits to print.
+        form: Custom format string for printing the numbers.
+        root: String to print before the number.
+        sep: Separator character between the numbers.
+        suffix: String to print after the number.
+        scale: Scale factor to multiply each number.
+        comma: Put commas between the outputs.
+        skipnmodm: Skip numbers with modulus.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `CountOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(COUNT_METADATA)
+    params = count_params(
+        bot=bot,
+        top=top,
+        step=step,
+        seed=seed,
+        sseed=sseed,
+        column=column,
+        digits=digits,
+        form=form,
+        root=root,
+        sep=sep,
+        suffix=suffix,
+        scale=scale,
+        comma=comma,
+        skipnmodm=skipnmodm,
+    )
+    return count_execute(params, execution)
+
+
+__all__ = [
+    "COUNT_METADATA",
+    "CountOutputs",
+    "CountParameters",
+    "count",
+    "count_params",
+]